Three species groups of Tragulus have been identified based on craniometric skull analyses and coat coloration patterns.

[8] Mouse-deer possess a triangular-shaped head, arched back, and round body with elevated rear quarters.

[6] It has been argued that Java mouse-deer are an “edge” species, favoring areas of dense vegetation along riverbanks.

[6] They are often classified as folivores, eating primarily leaves, shrubs, shoots, buds, and fungi, in addition to fruits which have fallen from trees.

To protect themselves and their mates or to defend their territory, mouse-deer slash rivals with their sharp, protruding canine “tusks.” It has also been observed that, when threatened, the Java mouse-deer will beat its hooves quickly against the ground, reaching speeds of up to 7 beats per second, creating a “drum roll” sound.

[6][13] However, some sources have observed that the breeding season for the Java mouse-deer in nature occurs from November to December.

[16] Additionally, female mouse-deer have the potential to be pregnant throughout most of their adult life, and they are capable of conceiving 85–155 minutes after giving birth.

[6][13] Typical litters consist of a single fawn, which resembles a miniature adult, although the tusk-like incisors prevalent in males are not visible in the young mouse-deer.

[6] The average mass of a newborn fawn is 370 grams (13 oz), and these precocial young are capable of standing within 30 minutes after birth.

[9] On average, it takes the young, both male and female, 167 days (~5 months) to reach sexual maturity.

Mouse-deer are particularly vulnerable to being hunted by humans at night because of their tendency to freeze when illuminated by having a spotlight shone on them.

[1] Because of the small size of the Java mouse-deer, dogs are also a common predator for them, as well as crocodiles, big cats, birds of prey, and snakes.

[18] Java mouse-deer is currently categorized as “Data Deficient” on the International Union for Conservation of Nature's Red List.

[1] Some conservation actions which have been implemented include legally protecting the species, which, although it has been in effect since 1931, makes no significant difference since hunting of Java mouse-deer still occurs.

Historically, the mouse-deer has featured prominently in Malay and Indonesian folklore, where it is considered a wise creature.